correlationMethExprs: Computes the correlation between methylation and expression

In MEAL: Perform methylation analysis

Description

Estimates the correlation between methylation and expression. When there are known variables that affect methylation and/or expression, their effect can be substracted using a linear model and then the residuals are used.

Usage

correlationMethExprs(
  multiset,
  meth_set_name = NULL,
  exprs_set_name = NULL,
  vars_meth = NULL,
  vars_exprs = NULL,
  sel_cpgs,
  flank = 250000,
  betas = TRUE,
  num_cores = 1,
  verbose = TRUE
)

Arguments

multiset	MultiDataSet containing a methylation and an expression slots.
meth_set_name	Character vector with the name of the MultiDataSet's slot containing methylation data.
exprs_set_name	Character vector with the name of the MultiDataSet's slot containing expression data.
vars_meth	Character vector with the names of the variables that will be used to obtain the methylation residuals. By default, none is used and residuals are not computed.
vars_exprs	Character vector with the names of the variables that will be used to obtain the expression residuals. By default, none is used and residuals are not computed.
sel_cpgs	Character vector with the name of the CpGs used in the analysis. If empty, all the CpGs of the methylation set will be used.
flank	Numeric with the number of pair bases used to define the cpg-expression probe pairs.
betas	If set is a GenomicRatioSet, should beta values be used? (Default: TRUE)
num_cores	Numeric with the number of cores to be used.
verbose	Logical value. If TRUE, it writes out some messages indicating progress. If FALSE nothing should be printed.

Details

For each cpg, a range is defined by the position of the cpg plus the flank parameter (upstream and downstream). Only those expression probes that are entirely in this range will be selected. For these reason, it is required that the ExpressionSet contains a featureData with the chromosome and the starting and ending positions of the probes.

Value

Data.frame with the results of the linear regression:

• cpg: Name of the cpg

• exprs: Name of the expression probe

• beta: coefficient of the methylation change

• se: standard error of the beta

• P.Value: p-value of the beta coefficient

• adj.P.Val: q-value computed using B&H

MEAL documentation built on Feb. 3, 2021, 2 a.m.